Kitamura is on his first visit to India after being appointed as the NSA.
"A pleasure to receive Japanese NSA Shigeru Kitamura on his first visit to India as the National Security Advisor. Good discussions on our foreign policy cooperation," Jaishankar tweeted.
The meeting between the two leaders comes days ahead of Japan Prime Minister Shinzo Abe visit to India.
India and Japan are expected to also hold first 2+2 ministerial meeting between the Foreign and Defence ministers later this month.
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